B.1.1.529 Omicron variant

[Woodchopper]

Thread concludes:

In summary this work suggests that Omicron does appear to have become more immune evasive, but that properties associated with disease progression *may* be attenuated to some extent. The significant growth of Omicron nevertheless represents a major public health challenge.

https://twitter.com/guptar_lab/status/1 ... 46628?s=21

This is the second finding which suggests how Omi might be less virulent.

But still early days, and if it is that may be offset by it infecting many more people.

[OffTheRock]

NHS hospitals in England 94% full before start of Omicron* surge

* - other reasons to be in hospital exist. But not for much longer.

Cos literally nobody predicted that having hospitals fuller than usual for the time of year going into winter would be an issue. And it’s definitely not going to be the government’s fault when it goes tits up, it’ll be omicron because no one could possibly have foreseen that either.

Is flu non-existent?

Heard nothing about it and I'm assuming no news is good news. A lot of vaccines plus a few weeks of voluntary lockdown is going to crush it, surely.

It’s fairly non-existent. The restrictions still going on in many southern hemispere countries over their winter probably kept the amount of flu circulating globally quite low. We can probably have a go at getting flu back with the non mask wearing and Xmas mixing and not staying at home when you are ill. If anyone can do it the UK can.

[Herainestold]

Neil Ferguson is predicting 5000 Omicron deaths per day.

Gloomy modelling from 'Professor Lockdown' today suggested there could be 5,000 Omicron deaths a day this winter without more restrictions as Britain's overall Covid cases rocketed to record levels for the third day in a row.

A total of 93,045 people tested positive for Covid in the past 24 hours, up 60 per cent in a week, but the ultra-virulent variant is thought to be doubling nationally every two days and spreading faster than testing can keep up.

In an early warning sign, coronavirus hospitalisations in Omicron hotspot London have spiked by more than a third in a week — although they are rising from a small base with just 199 admitted on Tuesday.

https://www.dailymail.co.uk/news/articl ... s-DAY.html

[lpm]

Any simple sense test shows 5,000 deaths in a day might be mathematically possible - but it would only be a single day. E.g. cases of 5,000,000 in a day, leading to the epidemic ending abruptly when the entire country has been infected.

Essentially a very high spike rules out an extended spike. A lower spike guarantees it will be extended. That's all we've got to play for against Omicron because it is unstoppable - delay to get more boosters and spread the hospitalisions across several weeks.

The complication for models is the feedback loop - cases are a function of restrictions, restrictions are a function of cases. People voluntarily lockdown when cases rise fast. Everyone becomes one degree of contact from a case so self isolate.

[shpalman]

Any simple sense test shows 5,000 deaths in a day might be mathematically possible - but it would only be a single day. E.g. cases of 5,000,000 in a day, leading to the epidemic ending abruptly when the entire country has been infected.

... just in time for the UK to get around to that "circuit breaker" they've started talking about.

[Woodchopper]

Any simple sense test shows 5,000 deaths in a day might be mathematically possible - but it would only be a single day. E.g. cases of 5,000,000 in a day, leading to the epidemic ending abruptly when the entire country has been infected.

Essentially a very high spike rules out an extended spike. A lower spike guarantees it will be extended. That's all we've got to play for against Omicron because it is unstoppable - delay to get more boosters and spread the hospitalisions across several weeks.

The complication for models is the feedback loop - cases are a function of restrictions, restrictions are a function of cases. People voluntarily lockdown when cases rise fast. Everyone becomes one degree of contact from a case so self isolate.

If the peak were 5 000 000 in a day then either large parts of the healthcare system would collapse as a significant proportion of essential personnel wouldn't be at work (due to being in quarantine or being unable to commute), or everyone would just turn up to work anyway in the absence of a positive test result (see the testing capacity thread) and they'd infect all the highly vulnerable patents.

But as you say, it would be unlikely to come to that as even in the absence of government restrictions people will alter their behaviour and reduce social contact.

[shpalman]

I think the UK's highest reported deaths in a single day was 1820 on the 20th of January this year, but the 7-day average peaked at about 1250. That followed a peak in the cases per day of about 60,000. That was the pre-vaccine CFR of 2%.

More recently we've had about 170 deaths per day at the end of October/beginning of November following a peak in the case rate of about 47,000 per day. CFR was therefore about 0.36%. The spiking cases now seem to be in the youngest age groups, so there won't be that many deaths unless/until older adults catch it from them.

Not looking that the Daily Mail link for longer than absolutely necessary, I couldn't see if they had also reported the case numbers their models generate anywhere, to see more directly what they'd be getting for the CFR under their assumptions. But it did seem like the headline figures are the peak values.

[shpalman]

Is it stuff from 2021-12-16-COVID19-Report-48.pdf which the newspaper is passing off as journalism and not copy-pasting? See Fig. 3 on page 17.

[shpalman]

There's a link to https://github.com/mrc-ide/global_covid_vaccine_booster in that pdf, there's this figure in there but it doesn't exactly match the figure in their pdf which they're referring to there.

fig2_incidence.png (88.49 KiB) Viewed 1649 times

... but maybe it can be compared to

fig2.png (208.76 KiB) Viewed 1649 times

which is similar to figures in the pdf except for the VFR values. But anyway if the middle graph is the one giving a peak of 5000 deaths per day (75 per million in a country of 66 million) then the peak case rate is about 25,000 per million per day i.e. 1.7 million in a country of 66 million.

So yeah, more or less wot you reckoned already, and yes it's a sharp peak, I'm not going to learn R just to figure out how to plot it myself on a zoomed-in x-axis.

[shpalman]

Any simple sense test shows 5,000 deaths in a day might be mathematically possible - but it would only be a single day. E.g. cases of 5,000,000 in a day, leading to the epidemic ending abruptly when the entire country has been infected.

... just in time for the UK to get around to that "circuit breaker" they've started talking about.

Post-Xmas lockdown 'too late', says Sage member

Note that the peaks in the ICL models are right at the beginning of 2022, so yeah do the circuit breaker after Christmas when it will be less disruptive it's fine.

[shpalman]

There's a link to https://github.com/mrc-ide/global_covid_vaccine_booster in that pdf, there's this figure in there but it doesn't exactly match the figure in their pdf which they're referring to there.

I've just noticed the bar charts which seem to give a total incidence per million of 2-4 million - see Figure S5 on page 32.

Do they really mean that everyone is going to catch it 3 times? Really? With hardly any effect from who gets boosted?

Of course they're not actually simulating the UK, just a country which is the UK and which is being used to make predictions about what might happen in the UK, but if their model for what is happening right now is obviously wrong then I don't really see why their prediction can suddenly become accurate about the future.

Even if the UK currently has about 1000 deaths per week, that's about 2 per million per day. You would barely even see that on the scale they're using in Figure 2, which goes up to 150, but by eye they seem to be saying there are 10 per million per day now and will peak at 50 per million per day. From Figure S5, this seems to correspond to a case rate of about 5000/million/day (3500/100,000/week) and I really wonder if you already had 330,000 cases per day earlier this season

Figure 2B does suggest that by boosting the oldest age group, the total deaths would only be about 300,000 instead of ~430,000.

[lpm]

Official lockdown on Monday 27 Dec seems possible, politically? The morons in the electorate will be praising Boris for "getting Christmas done". And headline cases could be extraordinary.

Of course that's a week too late. Not clear how strong the voluntary lockdown will be in the coming week - could be enough to scrape through this.

[shpalman]

Omicron is spreading rapidly in Italy, with new cases identified in both the north and south of the country, according to the national health institute (ISS).

The health agency reported that regional laboratories had so far identified 84 cases of new coronavirus variant on Saturday, “a strong acceleration” from 55 early on Friday, according to Reuters.

Thirty three cases were found in Lombardy, around Milan, in the north of Italy; 20 more were identified in Campania, the southern region centred on Naples.

Silvio Brusaferro, president of the ISS, said the spread of Omicron was “widely expected, in line with what we have seen in other countries, and we will probably see an increase in cases in coming days”.

... live blog

[shpalman]

Nearly 9,500 new cases of Omicron have been detected in England, according to the UK Health Security agency.

According to the latest figures released on Saturday, the number of confirmed Omicron cases stood at 23,168 - up 9,427 on the previous day’s total, figures from the UKHSA on Saturday showed.

Cases in Northern Ireland rose to 827, a rise of 514.

Scotland’s cases have reached 792, an increase of 96.

In Wales there are 181, up 22 on the previous day.

... live blog

oh and 7 people have died from it now

[bob sterman]

Comedy Carl "No Sign of a Second Wave" Heneghan is still pushing the "no sign of an omicron wave" line.

Apparently, the "Omicron Surge is Mostly Due to Ramping Up Testing and May Already Be Peaking"

https://twitter.com/carlheneghan/status ... 2435348480

[gosling]

Of course that's a week too late. Not clear how strong the voluntary lockdown will be in the coming week - could be enough to scrape through this.

We met a friend for lunch yesterday in Southwark. Considering it was the last Friday before Christmas Eve we assumed the restaurant would be busy and had thought about cancelling. Turned out we were the only ones there apart from the staff. The tube was still pretty busy though. So a semi-strong voluntary lockdown in London.

[Brightonian]

Was wondering just last night why cases in Ireland weren't increasing (indeed, I think they were decreasing).

This evening's news: 7,333 new cases, compared with 4,004 seven days ago. Presumably Omicron.

A few days ago the recommendation from health officials was that pubs, restaurants, theatres etc. should close at 5 p.m. each day. Personally I think they should be closed completely. Instead the government decided they should close at 8 p.m. And not immediately, but only from Monday.

[Trinucleus]

Was wondering just last night why cases in Ireland weren't increasing (indeed, I think they were decreasing).

This evening's news: 7,333 new cases, compared with 4,004 seven days ago. Presumably Omicron.

A few days ago the recommendation from health officials was that pubs, restaurants, theatres etc. should close at 5 p.m. each day. Personally I think they should be closed completely. Instead the government decided they should close at 8 p.m. And not immediately, but only from Monday.

My wife was in Dubllin last month, where you can't get in a bar or cafe without showing a vaccine passport. I understand that makes it a fascist state, though I don't think they've yet invaded Poland

[Herainestold]

Two obvious things
1) We need to shut down everything immediately
2) It won't happen.

[lpm]

3) Weekly clapping possibly won't be enough to sustain the NHS.

[Herainestold]

3) Weekly clapping possibly won't be enough to sustain the NHS.

At this point assume there is no NHS.
Protect yourself (and others) and prepare to die alone.

[Woodchopper]

Latest UK HSA risk assessment for Omicron:

There are insufficient data to fully assess severity, which is expected in the early period of emergence of a new variant. However, on the data available in the UK, there is no signal that supports a difference in the intrinsic virulence of the Omicron virus compared to Delta.

https://assets.publishing.service.gov.u ... .1.529.pdf

[Sciolus]

Severity is irrelevant when it spreads this fast.

[shpalman]

UKHSA

12,133 additional confirmed cases of the #Omicron variant of COVID-19 have been reported across the UK.

Confirmed Omicron cases in the UK now total 37,101.

[temptar]

Was wondering just last night why cases in Ireland weren't increasing (indeed, I think they were decreasing).

This evening's news: 7,333 new cases, compared with 4,004 seven days ago. Presumably Omicron.

A few days ago the recommendation from health officials was that pubs, restaurants, theatres etc. should close at 5 p.m. each day. Personally I think they should be closed completely. Instead the government decided they should close at 8 p.m. And not immediately, but only from Monday.

Some of those cases were back log. Today's number is ca 5000.

Current estimate is Omicron is ca 53% of cases. For Belgium, the most recent estimate is 11% which I assume will change with all those Brits trying to get into France via Belgium. I really don't know whether to travel or not